def find_place( self, a, distance, added_order=1):
"""tries to find accurate place for next atom around atom 'id',
returns x,y and list of ids of 'items' found there for overlap, those atoms are not bound to id"""
ids_bonds = a.neighbors
if len( ids_bonds) == 0:
x = a.x + cos( pi/6) *distance
y = a.y - sin( pi/6) *distance
elif len( ids_bonds) == 1:
neigh = ids_bonds[0]
if a.neighbor_edges[0].order != 3 and added_order != 3:
# we add a normal bond to atom with one normal bond
if a == self._last_used_atom or len( neigh.neighbors) != 2:
# the user has either deleted the last added bond and wants it to be on the other side
# or it is simply impossible to define a transoid configuration
self.sign = -self.sign
x = a.x + cos( self.get_angle( a, ids_bonds[0]) +self.sign*2*pi/3) *distance
y = a.y + sin( self.get_angle( a, ids_bonds[0]) +self.sign*2*pi/3) *distance
else:
# we would add the new bond transoid
neighs2 = neigh.neighbors
neigh2 = (neighs2[0] == a) and neighs2[1] or neighs2[0]
x = a.x + cos( self.get_angle( a, neigh) +self.sign*2*pi/3) *distance
y = a.y + sin( self.get_angle( a, neigh) +self.sign*2*pi/3) *distance
side = geometry.on_which_side_is_point( (neigh.x,neigh.y,a.x,a.y), (x,y))
if side == geometry.on_which_side_is_point( (neigh.x,neigh.y,a.x,a.y), (neigh2.x,neigh2.y)):
self.sign = -self.sign
x = a.x + cos( self.get_angle( a, neigh) +self.sign*2*pi/3) *distance
y = a.y + sin( self.get_angle( a, neigh) +self.sign*2*pi/3) *distance
self._last_used_atom = a
else:
x = a.x + cos( self.get_angle( a, ids_bonds[0]) + pi) *distance
y = a.y + sin( self.get_angle( a, ids_bonds[0]) + pi) *distance
else:
x, y = self.find_least_crowded_place_around_atom( a, range=distance)
return x, y
def _draw_second_line( self, coords):
my_x1, my_y1 = self.atom1.get_xy()
my_x2, my_y2 = self.atom2.get_xy()
my_coords = (my_x1,my_y1,my_x2,my_y2)
x, y, x0, y0 = coords
# shortening of the second bond
dx = x-x0
dy = y-y0
if self.center:
_k = 0
else:
_k = (1-self.double_length_ratio)/2
x, y, x0, y0 = x-_k*dx, y-_k*dy, x0+_k*dx, y0+_k*dy
# shift according to the bonds arround
side = geometry.on_which_side_is_point( my_coords, (x,y))
for atom in (self.atom1,self.atom2):
second_atom = atom is self.atom1 and self.atom2 or self.atom1
neighs = [n for n in atom.neighbors if geometry.on_which_side_is_point( my_coords, n.get_xy())==side and n is not second_atom]
for n in neighs:
dist2 = _k*geometry.point_distance(*my_coords)*geometry.on_which_side_is_point((atom.x, atom.y, n.x, n.y), (second_atom.x, second_atom.y))
xn1, yn1, xn2, yn2 = geometry.find_parallel( atom.x, atom.y, n.x, n.y, dist2)
xp,yp,parallel,online = geometry.intersection_of_two_lines( x,y,x0,y0,xn1,yn1,xn2,yn2)
if not parallel:
if not geometry.is_point_beween_points_of_line( (x,y,x0,y0),(xp,yp)):
# only shorten the line - do not elongate it
continue
if geometry.point_distance( atom.x,atom.y,x,y) < geometry.point_distance( atom.x,atom.y,x0,y0):
x,y = xp, yp
else:
x0,y0 = xp, yp
else:
# parallel
pass
return [self._create_line_with_transform( (x, y, x0, y0), width=self.line_width, fill=self.line_color)]
def _draw_second_line( self, coords):
my_x1, my_y1 = self.atom1.get_xy()
my_x2, my_y2 = self.atom2.get_xy()
my_coords = (my_x1,my_y1,my_x2,my_y2)
x, y, x0, y0 = coords
# shortening of the second bond
dx = x-x0
dy = y-y0
if self.center:
_k = 0
else:
_k = (1-self.double_length_ratio)/2
x, y, x0, y0 = x-_k*dx, y-_k*dy, x0+_k*dx, y0+_k*dy
# shift according to the bonds arround
side = geometry.on_which_side_is_point( my_coords, (x,y))
for atom in (self.atom1,self.atom2):
second_atom = atom is self.atom1 and self.atom2 or self.atom1
neighs = [n for n in atom.neighbors if geometry.on_which_side_is_point( my_coords, n.get_xy())==side and n is not second_atom]
for n in neighs:
dist2 = _k*geometry.point_distance(*my_coords)*geometry.on_which_side_is_point((atom.x, atom.y, n.x, n.y), (second_atom.x, second_atom.y))
xn1, yn1, xn2, yn2 = geometry.find_parallel( atom.x, atom.y, n.x, n.y, dist2)
xp,yp,parallel,online = geometry.intersection_of_two_lines( x,y,x0,y0,xn1,yn1,xn2,yn2)
if not parallel:
if not geometry.is_point_beween_points_of_line( (x,y,x0,y0),(xp,yp)):
# only shorten the line - do not elongate it
continue
if geometry.point_distance( atom.x,atom.y,x,y) < geometry.point_distance( atom.x,atom.y,x0,y0):
x,y = xp, yp
else:
x0,y0 = xp, yp
else:
# parallel
pass
return [self._create_line_with_transform( (x, y, x0, y0), width=self.line_width, fill=self.line_color)]
def find_place(self, a, distance, added_order=1):
"""tries to find accurate place for next atom around atom 'id',
returns x,y and list of ids of 'items' found there for overlap, those atoms are not bound to id"""
ids_bonds = a.neighbors
if len(ids_bonds) == 0:
x = a.x + cos(pi / 6) * distance
y = a.y - sin(pi / 6) * distance
elif len(ids_bonds) == 1:
neigh = ids_bonds[0]
if a.neighbor_edges[0].order != 3 and added_order != 3:
# we add a normal bond to atom with one normal bond
if a == self._last_used_atom or len(neigh.neighbors) != 2:
# the user has either deleted the last added bond and wants it to be on the other side
# or it is simply impossible to define a transoid configuration
self.sign = -self.sign
x = a.x + cos(
self.get_angle(a, ids_bonds[0]) +
self.sign * 2 * pi / 3) * distance
y = a.y + sin(
self.get_angle(a, ids_bonds[0]) +
self.sign * 2 * pi / 3) * distance
else:
# we would add the new bond transoid
neighs2 = neigh.neighbors
neigh2 = (neighs2[0] == a) and neighs2[1] or neighs2[0]
x = a.x + cos(
self.get_angle(a, neigh) +
self.sign * 2 * pi / 3) * distance
y = a.y + sin(
self.get_angle(a, neigh) +
self.sign * 2 * pi / 3) * distance
side = geometry.on_which_side_is_point(
(neigh.x, neigh.y, a.x, a.y), (x, y))
if side == geometry.on_which_side_is_point(
(neigh.x, neigh.y, a.x, a.y), (neigh2.x, neigh2.y)):
self.sign = -self.sign
x = a.x + cos(
self.get_angle(a, neigh) +
self.sign * 2 * pi / 3) * distance
y = a.y + sin(
self.get_angle(a, neigh) +
self.sign * 2 * pi / 3) * distance
self._last_used_atom = a
else:
x = a.x + cos(self.get_angle(a, ids_bonds[0]) + pi) * distance
y = a.y + sin(self.get_angle(a, ids_bonds[0]) + pi) * distance
else:
x, y = self.find_least_crowded_place_around_atom(a, range=distance)
return x, y
def mark_template_bond( self, b):
if b in self.edges:
atms = b.atom1.neighbors + b.atom2.neighbors
atms = misc.difference( atms, [b.atom1, b.atom2])
coords = [a.get_xy() for a in atms]
line = b.atom1.get_xy() + b.atom2.get_xy()
if sum(geometry.on_which_side_is_point(line, xy) for xy in coords) > 0:
self.t_bond_first = b.atom1
self.t_bond_second = b.atom2
else:
self.t_bond_first = b.atom2
self.t_bond_second = b.atom1
else:
raise ValueError("Submitted bond does not belong to this molecule.")
def mark_template_bond(self, b):
if b in self.edges:
atms = b.atom1.neighbors + b.atom2.neighbors
atms = misc.difference(atms, [b.atom1, b.atom2])
coords = [a.get_xy() for a in atms]
line = b.atom1.get_xy() + b.atom2.get_xy()
if sum(geometry.on_which_side_is_point(line, xy)
for xy in coords) > 0:
self.t_bond_first = b.atom1
self.t_bond_second = b.atom2
else:
self.t_bond_first = b.atom2
self.t_bond_second = b.atom1
else:
raise ValueError(
"Submitted bond does not belong to this molecule.")
def transform( self, tr):
if not self.item:
return
for i in [self.item] + self.second + self.third + self.items:
coords = self.paper.coords( i)
tr_coords = tr.transform_xy_flat_list( coords)
self.paper.coords( i, tuple( tr_coords))
if self.selector:
self.unselect()
self.select()
# we need to check if the sign of double bond width has not changed
# this happens during 3d rotation
if self.order == 2 and not self.center:
line = list( self.atom1.get_xy())
line += self.atom2.get_xy()
x, y = self.paper.coords( self.second[0])[0:2]
sign = geometry.on_which_side_is_point( line, (x,y))
if sign * self.bond_width < 0:
self.bond_width *= -1
def transform( self, tr):
if not self.item:
return
for i in [self.item] + self.second + self.third + self.items:
coords = self.paper.coords( i)
tr_coords = tr.transform_xy_flat_list( coords)
self.paper.coords( i, tuple( tr_coords))
if self.selector:
self.unselect()
self.select()
# we need to check if the sign of double bond width has not changed
# this happens during 3d rotation
if self.order == 2 and not self.center:
line = list( self.atom1.get_xy())
line += self.atom2.get_xy()
x, y = self.paper.coords( self.second[0])[0:2]
sign = geometry.on_which_side_is_point( line, (x,y))
if sign * self.bond_width < 0:
self.bond_width *= -1
def _compute_sign_and_center( self):
"""returns tuple of (sign, center) where sign is the default sign of the self.bond_width"""
# check if we need to transform 3D before computation
transform = None
for n in self.atom1.neighbors + self.atom2.neighbors:
# self.atom1 and self.atom2 are in this list as well
if n.z != 0:
# engage 3d transform prior to detection of where to draw
transform = self._get_3dtransform_for_drawing()
break
if transform:
for n in self.atom1.neighbors + self.atom2.neighbors:
n.transform( transform)
# /end of check
line = self.atom1.get_xy() + self.atom2.get_xy()
atms = self.atom1.neighbors + self.atom2.neighbors
atms = misc.difference( atms, [self.atom1, self.atom2])
coords = [a.get_xy() for a in atms]
# searching for circles
circles = 0
for ring in self.molecule.get_smallest_independent_cycles_dangerous_and_cached():
if self.atom1 in ring and self.atom2 in ring:
on_which_side = lambda xy: geometry.on_which_side_is_point( line, xy)
circles += sum(map(on_which_side, [a.get_xy() for a in ring if a not in self.atoms]))
if circles:
side = circles
else:
sides = [geometry.on_which_side_is_point( line, xy, threshold=0.1) for xy in coords]
side = sum(sides)
# on which side to put the second line
if side == 0 and (len(self.atom1.neighbors) == 1 or
len(self.atom2.neighbors) == 1):
# maybe we should center, but this is usefull only when one of the atoms has no other substitution
ret = (1 ,1)
else:
ret = None
if not circles:
# we center when both atoms have visible symbol and are not in circle
if self.atom1.show and self.atom2.show:
ret = (1, 1)
# recompute side with weighting of atom types
else:
for i in range( len( sides)):
if sides[i] and atms[i].__class__.__name__ == "atom":
if atms[i].symbol == 'H':
sides[i] *= 0.1 # this discriminates H
elif atms[i].symbol != 'C':
sides[i] *= 0.2 # this makes "non C" less then C but more then H
side = sum(sides)
if not ret:
if side < 0:
ret = (-1, 0)
else:
ret = (1, 0)
# transform back if necessary
if transform:
inv = transform.get_inverse()
for n in self.atom1.neighbors + self.atom2.neighbors:
n.transform( inv)
# /end of back transform
return ret
def _compute_sign_and_center( self):
"""returns tuple of (sign, center) where sign is the default sign of the self.bond_width"""
# check if we need to transform 3D before computation
transform = None
for n in self.atom1.neighbors + self.atom2.neighbors:
# self.atom1 and self.atom2 are in this list as well
if n.z != 0:
# engage 3d transform prior to detection of where to draw
transform = self._get_3dtransform_for_drawing()
break
if transform:
for n in self.atom1.neighbors + self.atom2.neighbors:
n.transform( transform)
# /end of check
line = self.atom1.get_xy() + self.atom2.get_xy()
atms = self.atom1.neighbors + self.atom2.neighbors
atms = misc.difference( atms, [self.atom1, self.atom2])
coords = [a.get_xy() for a in atms]
# searching for circles
circles = 0
for ring in self.molecule.get_smallest_independent_cycles_dangerous_and_cached():
if self.atom1 in ring and self.atom2 in ring:
on_which_side = lambda xy: geometry.on_which_side_is_point( line, xy)
circles += sum(map(on_which_side, [a.get_xy() for a in ring if a not in self.atoms]))
if circles:
side = circles
else:
sides = [geometry.on_which_side_is_point( line, xy, threshold=0.1) for xy in coords]
side = sum(sides)
# on which side to put the second line
if side == 0 and (len(self.atom1.neighbors) == 1 or
len(self.atom2.neighbors) == 1):
# maybe we should center, but this is usefull only when one of the atoms has no other substitution
ret = (1 ,1)
else:
ret = None
if not circles:
# we center when both atoms have visible symbol and are not in circle
if self.atom1.show and self.atom2.show:
ret = (1, 1)
# recompute side with weighting of atom types
else:
for i in range( len( sides)):
if sides[i] and atms[i].__class__.__name__ == "atom":
if atms[i].symbol == 'H':
sides[i] *= 0.1 # this discriminates H
elif atms[i].symbol != 'C':
sides[i] *= 0.2 # this makes "non C" less then C but more then H
side = sum(sides)
if ret is None:
if side < 0:
ret = (-1, 0)
else:
ret = (1, 0)
# transform back if necessary
if transform:
inv = transform.get_inverse()
for n in self.atom1.neighbors + self.atom2.neighbors:
n.transform( inv)
# /end of back transform
return ret
